VoltRon

Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration

Website | Tutorials | Preprint

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VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is also capable of analyzing multiple types of spatially-aware data modalities.

Staying up-to-date

To ask questions please use VoltRon discussion forum on google groups.

• https://groups.google.com/forum/#!forum/voltron_discussion

Installation

Install from the GitHub repository using devtools (with R version 4.3.0 or higher):

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("BIMSBbioinfo/VoltRon")

Depending on the number of required dependencies, installation may be completed under a minute or may take a few minutes.

On Windows and MacOS, OpenCV will be downloaded automatically upon installation. However, Rtools may be required to be downloaded too, hence this may take some time!

On Ubuntu we provide a set of instructions that may help users to build OpenCV with necessary headers here.

On Fedora you may need opencv-devel:

yum install opencv-devel

Dependencies

RBioformats

VoltRon incorporates RBioformats package to import images from ome.tiff files, which requires Java JDK to be available in your system:

See https://cran.r-project.org/web/packages/rJava below for more information.

Rarr

We also use a specific version of the Rarr package geared towards reading and writing missing data types (e.g. character). We will use the standard Rarr package once modifications are released to Bioconductor. Thus please use:

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("Huber-group-EMBL/Rarr")

SimpleITK

VoltRon incorporates the SimpleITK package to execute non-rigid alignment across assays. You can install SimpleITK from GitHub using the following command.

Depending on the number of processors the user has, you can modify the MAKEJ=6 argument. We also need SimpleElastix module of SimpleITK to be installed, hence we add -DSimpleITK_USE_ELASTIX=ON to the ADDITIONAL_SITK_MODULES argument.

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github(
  repo = "SimpleITK/SimpleITKRInstaller", 
  configure.vars=c("MAKEJ=6", 
                   "ADDITIONAL_SITK_MODULES=-DSimpleITK_USE_ELASTIX=ON"))

For more information, plase visit the SimpleITK website.

Docker Hub

You can also run VoltRon from a container already available in Docker Hub. The docker image is based on the Rocker Project and can be run from the terminal like below:

docker run --rm -ti -e PASSWORD=<yourpassword> -p 8787:8787 amanukyan1385/rstudio-voltron:main

Then, start the RStudio session from the browser at http://localhost:8787/ and enter rstudio as username and <yourpassword> as password.

See here for more instructions on how to run the container using Docker Desktop.

References

Manukyan, A., Bahry, E., Wyler, E., Becher, E., Pascual-Reguant, A., Plumbom, I., ... & Akalin, A. (2023). VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration. bioRxiv, 2023-12.